Locus 1261

Sequence ID	2R_DroMel_CAF1
Location	4,924,849 – 4,924,967
Length	118
Max. P	0.632732

overview

Window 7

Location	4,924,849 – 4,924,942
Length	93
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	87.61
Mean single sequence MFE	-23.68
Consensus MFE	-18.85
Energy contribution	-19.77
Covariance contribution	0.92
Combinations/Pair	1.08
Mean z-score	-2.20
Structure conservation index	0.80
SVM decision value	0.20
SVM RNA-class probability	0.632732
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4924849 93 + 20766785
AUACGUACGUACUUUCCUUCGCUGGCUUUUCGCAAUUUGUUUAUGUGACCAUCAAUUUGUGAGGCUCCACAGACAC-UUUGUGUUUGCCGGCCA
.(((....))).........((((((....(((((..(((((.((.((((.(((.....))))).)))).))))).-.)))))...)))))).. ( -26.80)
>DroSec_CAF1 13697 87 + 1
------ACGUACUUUCGUUCGCUGGCUUUUCGCAAUUUGUUUAUGUGACCAUCAAUUUGUGAGGCUCCACAGACAC-UUUGUGUUUGCCGGCCA
------(((......)))..((((((....(((((..(((((.((.((((.(((.....))))).)))).))))).-.)))))...)))))).. ( -26.90)
>DroSim_CAF1 13865 87 + 1
------ACGUACUUUUUUUCGCUGGUCUUUCGCAAUUUGUUUAUGUGACCAUCAAUUUGUGAGGCUCCACAGACAC-UUUGUGUUUGCCGGCCA
------..............((((((....(((((..(((((.((.((((.(((.....))))).)))).))))).-.)))))...)))))).. ( -24.30)
>DroEre_CAF1 11952 87 + 1
------ACGUACUUUUGUUCGCUGGUUUUUCGCAGUUUGUUUAUGUGACCAUCAAUUUGUGAGGCUCCACAGACAC-UUUGUGUUUGCCGGCCA
------..............((((((....(((((..(((((.((.((((.(((.....))))).)))).))))).-.)))))...)))))).. ( -24.70)
>DroYak_CAF1 13947 86 + 1
-------CGUACAUUCGUUCGCUGGGUUUUCGCAAUUUGUUUAUGUGACCAUCAAUUUGUGAGGCUCCACAGACAC-UUUGUGUUUGCCGGCCA
-------.............(((((.....(((((..(((((.((.((((.(((.....))))).)))).))))).-.)))))....))))).. ( -22.30)
>DroAna_CAF1 10797 83 + 1
------ACACACCAUCAGCCAC-----AUUCGCAAUUUGUUUAUGCGACCAUCAAUUCGUGAAGCUCCACAGACACACUUGUGUUUGCCGGCCA
------...........(((..-----..(((((.........))))).....................(((((((....)))))))..))).. ( -17.10)
>consensus
______ACGUACUUUCGUUCGCUGGCUUUUCGCAAUUUGUUUAUGUGACCAUCAAUUUGUGAGGCUCCACAGACAC_UUUGUGUUUGCCGGCCA
....................((((((....(((((..(((((.((.((((.(((.....))))).)))).)))))...)))))...)))))).. (-18.85 = -19.77 +   0.92)

alignment

secondary structure

dotplot

Window 8

Location	4,924,872 – 4,924,967
Length	95
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	82.36
Mean single sequence MFE	-26.53
Consensus MFE	-15.41
Energy contribution	-16.42
Covariance contribution	1.00
Combinations/Pair	1.28
Mean z-score	-2.19
Structure conservation index	0.58
SVM decision value	0.05
SVM RNA-class probability	0.559841
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4924872 95 - 20766785
AU------CUUGGCCAUUUUAUCGAUUUGCU-----UGGCCGGCAAACACAAA-GUGUCUGUGGAGCCUCACAAAUUGAUGGUCACAUAAACAAAUUGCGAAAAGCC
..------..((((((.....((((((((..-----.((((.(((.((((...-)))).))).).)))...))))))))))))))............((.....)). ( -27.20)
>DroPse_CAF1 11817 103 - 1
AUUUGUUACCUCUCGAUUUUAUUGAUUUGCUUGGCUUGGCCGGCAAACACAAA-AGUGCUCCACCGCCUCCAAAUUUGGCGGUCACGUAAACAAAU---GAAAAUCG
.............(((((((.(((.((((((.(((...)))))))))......-.(((....((((((.........))))))))).....)))..---.))))))) ( -26.30)
>DroSim_CAF1 13882 95 - 1
AU------CUUGGCCAUUUUAUCGAUUUGCU-----UGGCCGGCAAACACAAA-GUGUCUGUGGAGCCUCACAAAUUGAUGGUCACAUAAACAAAUUGCGAAAGACC
..------..((((((.....((((((((..-----.((((.(((.((((...-)))).))).).)))...)))))))))))))).............(....)... ( -27.30)
>DroEre_CAF1 11969 95 - 1
AU------CUUGGCCAUUUUAUCGAUUUGCU-----UGGCCGGCAAACACAAA-GUGUCUGUGGAGCCUCACAAAUUGAUGGUCACAUAAACAAACUGCGAAAAACC
..------..((((((.....((((((((..-----.((((.(((.((((...-)))).))).).)))...))))))))))))))...................... ( -26.40)
>DroYak_CAF1 13963 95 - 1
AU------CUUGGCCAUUUUAUCGAUUUGCU-----UGGCCGGCAAACACAAA-GUGUCUGUGGAGCCUCACAAAUUGAUGGUCACAUAAACAAAUUGCGAAAACCC
..------..((((((.....((((((((..-----.((((.(((.((((...-)))).))).).)))...))))))))))))))...................... ( -26.40)
>DroAna_CAF1 10813 92 - 1
AG------CUCCGCUAUUUUAUUGAUUUGCU-----UGGCCGGCAAACACAAGUGUGUCUGUGGAGCUUCACGAAUUGAUGGUCGCAUAAACAAAUUGCGAAU----
..------..........((((..(((((..-----.((((.(((.((((....)))).))).).)))...)))))..))))(((((.........)))))..---- ( -25.60)
>consensus
AU______CUUGGCCAUUUUAUCGAUUUGCU_____UGGCCGGCAAACACAAA_GUGUCUGUGGAGCCUCACAAAUUGAUGGUCACAUAAACAAAUUGCGAAAAACC
..........((((((.....((((((((........((((.(((.((((....)))).))).).)))...))))))))))))))...................... (-15.41 = -16.42 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:22 2006